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  1. Artikel ; Online: Current annotation strategies for T cell phenotyping of single-cell RNA-seq data.

    Mullan, Kerry A / de Vrij, Nicky / Valkiers, Sebastiaan / Meysman, Pieter

    Frontiers in immunology

    2023  Band 14, Seite(n) 1306169

    Abstract: Single-cell RNA sequencing (scRNA-seq) has become a popular technique for interrogating the diversity and dynamic nature of cellular gene expression and has numerous advantages in immunology. For example, scRNA-seq, in contrast to bulk RNA sequencing, ... ...

    Abstract Single-cell RNA sequencing (scRNA-seq) has become a popular technique for interrogating the diversity and dynamic nature of cellular gene expression and has numerous advantages in immunology. For example, scRNA-seq, in contrast to bulk RNA sequencing, can discern cellular subtypes within a population, which is important for heterogenous populations such as T cells. Moreover, recent advancements in the technology allow the parallel capturing of the highly diverse T-cell receptor (TCR) sequence with the gene expression. However, the field of single-cell RNA sequencing data analysis is still hampered by a lack of gold-standard cell phenotype annotation. This problem is particularly evident in the case of T cells due to the heterogeneity in both their gene expression and their TCR. While current cell phenotype annotation tools can differentiate major cell populations from each other, labelling T-cell subtypes remains problematic. In this review, we identify the common automated strategy for annotating T cells and their subpopulations, and also describe what crucial information is still missing from these tools.
    Mesh-Begriff(e) T-Lymphocytes ; Single-Cell Gene Expression Analysis ; Data Analysis ; Sequence Analysis, RNA ; Receptors, Antigen, T-Cell/genetics
    Chemische Substanzen Receptors, Antigen, T-Cell
    Sprache Englisch
    Erscheinungsdatum 2023-12-21
    Erscheinungsland Switzerland
    Dokumenttyp Journal Article ; Review ; Research Support, Non-U.S. Gov't
    ZDB-ID 2606827-8
    ISSN 1664-3224 ; 1664-3224
    ISSN (online) 1664-3224
    ISSN 1664-3224
    DOI 10.3389/fimmu.2023.1306169
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  2. Artikel: HLA-DRB1 Alleles Associated with Lower Leishmaniasis Susceptibility Share Common Amino Acid Polymorphisms and Epitope Binding Repertoires.

    de Vrij, Nicky / Meysman, Pieter / Gielis, Sofie / Adriaensen, Wim / Laukens, Kris / Cuypers, Bart

    Vaccines

    2021  Band 9, Heft 3

    Abstract: Susceptibility for leishmaniasis is largely dependent on host genetic and immune factors. Despite the previously described association of human leukocyte antigen (HLA) gene cluster variants as genetic susceptibility factors for leishmaniasis, little is ... ...

    Abstract Susceptibility for leishmaniasis is largely dependent on host genetic and immune factors. Despite the previously described association of human leukocyte antigen (HLA) gene cluster variants as genetic susceptibility factors for leishmaniasis, little is known regarding the mechanisms that underpin these associations. To better understand this underlying functionality, we first collected all known leishmaniasis-associated HLA variants in a thorough literature review. Next, we aligned and compared the protection- and risk-associated HLA-DRB1 allele sequences. This identified several amino acid polymorphisms that distinguish protection- from risk-associated HLA-DRB1 alleles. Subsequently, T cell epitope binding predictions were carried out across these alleles to map the impact of these polymorphisms on the epitope binding repertoires. For these predictions, we used epitopes derived from entire proteomes of multiple
    Sprache Englisch
    Erscheinungsdatum 2021-03-17
    Erscheinungsland Switzerland
    Dokumenttyp Journal Article
    ZDB-ID 2703319-3
    ISSN 2076-393X
    ISSN 2076-393X
    DOI 10.3390/vaccines9030270
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  3. Artikel ; Online: Persistent T cell unresponsiveness associated with chronic visceral leishmaniasis in HIV-coinfected patients.

    de Vrij, Nicky / Pollmann, Julia / Rezende, Antonio M / Ibarra-Meneses, Ana V / Pham, Thao-Thy / Hailemichael, Wasihun / Kassa, Mekibib / Bogale, Tadfe / Melkamu, Roma / Yeshanew, Arega / Mohammed, Rezika / Diro, Ermias / Maes, Ilse / Domagalska, Malgorzata A / Landuyt, Hanne / Vogt, Florian / van Henten, Saskia / Laukens, Kris / Cuypers, Bart /
    Meysman, Pieter / Beyene, Hailemariam / Sisay, Kasaye / Kibret, Aderajew / Mersha, Dagnew / Ritmeijer, Koert / van Griensven, Johan / Adriaensen, Wim

    Communications biology

    2024  Band 7, Heft 1, Seite(n) 524

    Abstract: A large proportion of HIV-coinfected visceral leishmaniasis (VL-HIV) patients exhibit chronic disease with frequent VL recurrence. However, knowledge on immunological determinants underlying the disease course is scarce. We longitudinally profiled the ... ...

    Abstract A large proportion of HIV-coinfected visceral leishmaniasis (VL-HIV) patients exhibit chronic disease with frequent VL recurrence. However, knowledge on immunological determinants underlying the disease course is scarce. We longitudinally profiled the circulatory cellular immunity of an Ethiopian HIV cohort that included VL developers. We show that chronic VL-HIV patients exhibit high and persistent levels of TIGIT and PD-1 on CD8
    Mesh-Begriff(e) Humans ; Leishmaniasis, Visceral/immunology ; Leishmaniasis, Visceral/complications ; Leishmaniasis, Visceral/parasitology ; HIV Infections/immunology ; HIV Infections/complications ; Coinfection/immunology ; Male ; Adult ; Female ; CD8-Positive T-Lymphocytes/immunology ; Middle Aged ; Chronic Disease ; CD4-Positive T-Lymphocytes/immunology ; Ethiopia
    Sprache Englisch
    Erscheinungsdatum 2024-05-03
    Erscheinungsland England
    Dokumenttyp Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 2399-3642
    ISSN (online) 2399-3642
    DOI 10.1038/s42003-024-06225-2
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  4. Artikel ; Online: Lack of functional TCR-epitope interaction is associated with herpes zoster through reduced downstream T cell activation.

    Boeren, Marlies / de Vrij, Nicky / Ha, My K / Valkiers, Sebastiaan / Souquette, Aisha / Gielis, Sofie / Kuznetsova, Maria / Schippers, Jolien / Bartholomeus, Esther / Van den Bergh, Johan / Michels, Nele / Aerts, Olivier / Leysen, Julie / Bervoets, An / Lambert, Julien / Leuridan, Elke / Wens, Johan / Peeters, Karin / Emonds, Marie-Paule /
    Elias, George / Vandamme, Niels / Jansens, Hilde / Adriaensen, Wim / Suls, Arvid / Vanhee, Stijn / Hens, Niel / Smits, Evelien / Van Damme, Pierre / Thomas, Paul G / Beutels, Philippe / Ponsaerts, Peter / Van Tendeloo, Viggo / Delputte, Peter / Laukens, Kris / Meysman, Pieter / Ogunjimi, Benson

    Cell reports

    2024  Band 43, Heft 4, Seite(n) 114062

    Abstract: The role of T cell receptor (TCR) diversity in infectious disease susceptibility is not well understood. We use a systems immunology approach on three cohorts of herpes zoster (HZ) patients and controls to investigate whether TCR diversity against ... ...

    Abstract The role of T cell receptor (TCR) diversity in infectious disease susceptibility is not well understood. We use a systems immunology approach on three cohorts of herpes zoster (HZ) patients and controls to investigate whether TCR diversity against varicella-zoster virus (VZV) influences the risk of HZ. We show that CD4
    Mesh-Begriff(e) Humans ; Herpes Zoster/immunology ; Herpes Zoster/virology ; Receptors, Antigen, T-Cell/metabolism ; Receptors, Antigen, T-Cell/immunology ; Lymphocyte Activation/immunology ; Herpesvirus 3, Human/immunology ; Female ; Middle Aged ; Male ; CD4-Positive T-Lymphocytes/immunology ; Aged ; Adult ; Epitopes, T-Lymphocyte/immunology
    Chemische Substanzen Receptors, Antigen, T-Cell ; Epitopes, T-Lymphocyte
    Sprache Englisch
    Erscheinungsdatum 2024-04-07
    Erscheinungsland United States
    Dokumenttyp Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
    ZDB-ID 2649101-1
    ISSN 2211-1247 ; 2211-1247
    ISSN (online) 2211-1247
    ISSN 2211-1247
    DOI 10.1016/j.celrep.2024.114062
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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